CAP3

CAP3 is an online tool. In the present work CAP3 was used in genome annotation and to find the contigs. The CAP3 program includes a number of improvements and new features. The program has a capability to clip 58 and 38 low-quality regions of reads. It uses base quality values in computation of overlaps between reads, construction of multiple sequence alignments of reads, and generation of consensus sequences. The program also uses forward–reverse constraints to correct assembly errors and link contigs. An unusual feature of CAP3 is the use of forward-reverse constraints in the construction of contigs. Sequencing of both ends of a subclone often produces a forward-reverse constraint. A forward-reverse constraint specifies that the two reads should be on the opposite strands of the DNA molecule within a specified range of distance.